ROMA: an in vitro approach to defining target genes for transcription regulators.
We describe an in vitro transcription-based method called ROMA (run-off transcription-microarray analysis) for the genome-wide analysis of transcription regulated by sigma factors and other transcriptional regulators. ROMA uses purified RNA polymerase with and without a regulatory protein to monitor products of transcription from a genomic DNA template. Transcribed RNA is converted to cDNA and hybridized to gene arrays allowing for the identification of genes that are specifically activated by the regulator. We discuss the use of ROMA to define sigma factor regulons in Bacillus subtilis and its broad application to defining regulons for other transcriptional regulators in various species.
Maclellan
Shawn R
SR
Department of Microbiology, Cornell University, 327 Wing Hall, Ithaca, NY 14853-8101, USA.
Eiamphungporn
Warawan
W
Helmann
John D
JD
D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008967:Molecular Biology / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D018085:Regulon / Q000235:genetics; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
D012808:Sigma Factor; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases